Commits · e7e6eebc049b4d8bd58bef1fbd23c5c82120a6da · tsoc / openmm

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29 Apr, 2013 2 commits
- fixes fft thread divergence, makes hd 6xxx 5xxx cards work · e7e6eebc
  Yutong Zhao authored Apr 29, 2013
  
  e7e6eebc
- Ensure Python interpreter lock gets reacquired when an exception is thrown. · d96606e2
  Peter Eastman authored Apr 29, 2013
  
  d96606e2
26 Apr, 2013 2 commits
- Updating documentation for 5.1 · 53d469c5
  Peter Eastman authored Apr 26, 2013
  
  53d469c5
- Fixed thread synchronization problem in RPMD kernels · 647b2ea1
  Peter Eastman authored Apr 26, 2013
  
  647b2ea1
25 Apr, 2013 4 commits
- Fixed bugs in AMD specific code for CCMA · 27777280
  Peter Eastman authored Apr 25, 2013
  
  27777280
- OpenCL double precision RPMD test was not being run · 87b06907
  Peter Eastman authored Apr 25, 2013
  
  87b06907
- Fixed thread synchronization problem in RPMD kernels · bcf9f9b4
  Peter Eastman authored Apr 25, 2013
  
  bcf9f9b4
- Disabled peer-to-peer communication, since it currently makes things slower · 95696f7a
  Peter Eastman authored Apr 25, 2013
  
  95696f7a
24 Apr, 2013 5 commits
- Improved documentation for loadBondDefinitions() · b2ac07ad
  Peter Eastman authored Apr 24, 2013
  
  b2ac07ad
- Allow GBSA definitions to be split between multiple files · 77e2ddf4
  Peter Eastman authored Apr 24, 2013
  
  77e2ddf4
- Updated Lepton User Manual · 52c7a1fc
  Peter Eastman authored Apr 24, 2013
  
  52c7a1fc
- Fixed bug caused by missing synchronization in findInteractingBlocks() · 81753737
  Peter Eastman authored Apr 24, 2013
  
  81753737
- Changes to read more PDB files with nucleic acids correctly · aa4dad89
  Peter Eastman authored Apr 24, 2013
  
  aa4dad89
23 Apr, 2013 3 commits
- fixes another argument that was off by 1 · f472d424
  Yutong Zhao authored Apr 23, 2013
  
  f472d424
- Fixed some incorrect argument indices · 4e9167d0
  Peter Eastman authored Apr 23, 2013
  
  4e9167d0
- Workaround for bug in AMD's OpenCL for Linux · 74ba76fc
  Peter Eastman authored Apr 23, 2013
  
  74ba76fc
22 Apr, 2013 2 commits
- Optimizations to CustomIntegrator to prevent unnecessary extra force evaluations · 8eba00a7
  Peter Eastman authored Apr 22, 2013
  
  8eba00a7
- Fixed bugs in serializing State from Python · 0665e20b
  Peter Eastman authored Apr 22, 2013
  
  0665e20b
19 Apr, 2013 2 commits
- Fixes a hard to catch bug when a boundingBoxSize increases in size in between... · 282c6f2c
  Yutong Zhao authored Apr 19, 2013
```
Fixes a hard to catch bug when a boundingBoxSize increases in size in between a timestep, but does not trigger a rebuild of the neighbourlist. Affects the usage of singlePeriodicCopy in nonbonded force.  
```
  282c6f2c
- Bug fix when using peer-to-peer communication · ce2cd27b
  Peter Eastman authored Apr 19, 2013
  
  ce2cd27b
17 Apr, 2013 3 commits
- Created simulateGromacs.py example · 5e6d705e
  Peter Eastman authored Apr 17, 2013
  
  5e6d705e
- Bug fixes · e4b38cce
  Peter Eastman authored Apr 17, 2013
  
  e4b38cce
- Context.setState() works in Python · efa09228
  Peter Eastman authored Apr 17, 2013
  
  efa09228
16 Apr, 2013 3 commits
- Fixed bugs in reading Gromacs files · c4e9dcd2
  Peter Eastman authored Apr 16, 2013
  
  c4e9dcd2
- Updated version number to 5.1. · 456b8a05
  Peter Eastman authored Apr 16, 2013
  
  456b8a05
- Fixed bug that caused some TOP files to fail · 681f601b
  Peter Eastman authored Apr 16, 2013
  
  681f601b
15 Apr, 2013 5 commits
- Context constructor now uses const System&, guaranteeing that System won't be modified. · 0307a0db
  Yutong Zhao authored Apr 15, 2013
  
  0307a0db
- Fixes a minor windows compiler invocation issue where C:\Program Files becomes... · 19757775
  Yutong Zhao authored Apr 15, 2013
```
Fixes a minor windows compiler invocation issue where C:\Program Files becomes delimited by the space. Also enables debugging libraries to be built in debug mode for WIN32 + Visual Studio. 
```
  19757775
- CMakeLists now includes .cl and .cu kernel files as part of the project in Visual Studio. · 5c4abf73
  Yutong Zhao authored Apr 15, 2013
  
  5c4abf73
- Fixed bug that prevented constraints being applied when computing kinetic energy · 37b86c10
  Peter Eastman authored Apr 15, 2013
  
  37b86c10
- Fixes a race condition in buffer status in findBlocksWithInteractions() · 29256dfe
  Yutong Zhao authored Apr 15, 2013
  
  29256dfe
12 Apr, 2013 4 commits
- Updated version number to 5.1 · cbc21173
  Peter Eastman authored Apr 12, 2013
  
  cbc21173
- Call cudaProfilerStop() when destroying a context so profiling will work correctly · 11b86e0d
  Peter Eastman authored Apr 12, 2013
  
  11b86e0d
- Fixed errors in mixed precision mode · a106d7d1
  Peter Eastman authored Apr 12, 2013
  
  a106d7d1
- When computing kinetic energy, make sure the shifted velocities are... · 820a6baa
  Peter Eastman authored Apr 12, 2013
```
When computing kinetic energy, make sure the shifted velocities are perpendicular to the constraints
```
  820a6baa
11 Apr, 2013 1 commit
- Changed workgroup size to work around NVIDIA bug. This also improves performance slightly. · 01afee8b
  Peter Eastman authored Apr 11, 2013
  
  01afee8b
10 Apr, 2013 3 commits
- Added volatile keyword to fix crashes on some GPUs · 83284ce6
  Peter Eastman authored Apr 10, 2013
  
  83284ce6
- RPMD supports virtual sites · 3e7616fc
  Peter Eastman authored Apr 10, 2013
  
  3e7616fc
- Added some PDB residue and atom synonyms used by Tinker · 63955548
  Peter Eastman authored Apr 10, 2013
  
  63955548
09 Apr, 2013 1 commit
- RPMDIntegrator throws an exception if the System includes virtual sites · d5b80604
  Peter Eastman authored Apr 09, 2013
  
  d5b80604